PUBLICATION SPOTLIGHT - Single cell proteomics detects heterogeneity in complex cell systems

By Benjamin Furtwängler, PhD fellow, Porse Group

How would you summarise your study in one sentence?

We present a comprehensive mass spectrometry-based single-cell proteomics workflow that enables the characterization of complex cellular systems by quantifying the expression of over 1000 proteins in single-cells.

Can you describe briefly what you have explored and how?

We composed the workflow using the state of the art mass spectrometry technology combined with a FACS compatible sample preparation and computational data analysis pipeline. We subsequently benchmarked the workflow to investigate its capabilities to detect changes in protein expression between different celltypes. Finally, we applied the workflow to an exciting model system where we could successfully describe the cellular hierarchy and differentiation trajectories based on the single-cell protein expression data and even find evidence for an unexpected alternative trajectory.

What would you say is the novelty in this study?

With this study, we show that single-cell proteomics is ready to be scaled up to similar extends as some single-cell RNA sequencing methods, with the advantage of providing meaningful information about the actual protein expression. The readout of the protein expression is important as these molecules ultimately fulfil the function of the gene, and mRNA is only an intermediate product in the cell. Furthermore, with the integration of FACS in our workflow, we add another dimension of single-cell readout that has proven to be very valuable for deciphering complex cellular systems. Additionally, our computational pipeline provides the tools needed to make sense of this multidimensional data.

How do the results relate to the scientific field with respect to what is already known?

The potential of single-cell proteomics has been revealed multiple times and incremental technological improvements were extensively discussed. Nonetheless, bringing these parts together in such a comprehensive manner and benchmarking the workflow with an experimental setup that closely resembles its future application will likely be a very important step in moving this field forward.

Can you describe the potential of the findings beyond the research field?

Similar to single-cell RNA sequencing, the introduction of a new analytical technology might facilitate new findings in many areas of biology. Large-scale characterizations of complex cellular systems using single-cell proteomics and potentially in combination with multi-omics approaches might reveal previously unknown cell states or differentiation trajectories. Additionally, measuring differences of protein and RNA expression, might reveal important post-transcriptional gene regulation mechanisms.

For example, the hematopoietic system is immensely important for the human health and it is maintained by an interplay of many different celltypes serving specific functions. Treatment of diseases thereof, like acute myeloid leukemia, remains challenging, as the underlying mechanisms have yet to be fully understood. Single-cell proteomics might add the additional dimension of information that is needed to elucidate the mechanisms of such malignancies.

What are the next stages in this research?

In the next stages, we want to apply the single-cell proteomics workflow to the hematopoietic system in the bone marrow and characterize health and disease on protein level and compare these results with other -omics approaches. Moreover, we continuously work on technological improvements to further increase the proteome depth of our workflow.

Read full publication here: "Quantitative single-cell proteomics as a tool to characterize cellular hierarchies"